org.jmol.jvxl.readers
Class VolumeFileReader
java.lang.Object
org.jmol.jvxl.readers.VoxelReader
org.jmol.jvxl.readers.VolumeFileReader
- All Implemented Interfaces:
- VertexDataServer
- Direct Known Subclasses:
- ApbsReader, CubeReader, JaguarReader, JvxlReader, PltFormattedReader, XplorReader
class VolumeFileReader
- extends VoxelReader
Fields inherited from class org.jmol.jvxl.readers.VoxelReader |
ANGSTROMS_PER_BOHR, cJvxlEdgeNaN, colorEncoder, colorFractionBase, colorFractionRange, contourVertexCount, defaultColorFractionBase, defaultColorFractionRange, defaultCutoff, defaultEdgeFractionBase, defaultEdgeFractionRange, defaultMappedDataMax, defaultMappedDataMin, edgeFractionBase, edgeFractionRange, fractionData, fReturn, isApbsDx, isJvxl, isProgressive, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, marchingSquares, meshData, meshDataServer, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, sg, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData |
Methods inherited from class org.jmol.jvxl.readers.VoxelReader |
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, excludeMaximumSet, excludeMinimumSet, getCalcPoint, getColorIndexFromPalette, getColorPhaseIndex, getMaxMappedValue, getMinMappedValue, getSurfacePointIndex, gotoAndReadVoxelData, initializeVolumetricData, isInside, jvxlUpdateInfo, readColorData, readSurfacePoint, resetIsosurface, selectPocket, setVolumeData, updateSurfaceData, updateTriangles |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
br
protected java.io.BufferedReader br
endOfData
protected boolean endOfData
negativeAtomCount
protected boolean negativeAtomCount
atomCount
protected int atomCount
nSurfaces
private int nSurfaces
isAngstroms
protected boolean isAngstroms
canDownsample
protected boolean canDownsample
downsampleRemainders
private int[] downsampleRemainders
line
java.lang.String line
next
int[] next
VolumeFileReader
VolumeFileReader(SurfaceGenerator sg,
java.io.BufferedReader br)
determineFileType
static java.lang.String determineFileType(java.io.BufferedReader bufferedReader)
discardTempData
void discardTempData(boolean discardAll)
- Overrides:
discardTempData
in class VoxelReader
readVolumeParameters
void readVolumeParameters()
- Specified by:
readVolumeParameters
in class VoxelReader
readVolumeData
void readVolumeData(boolean isMapData)
- Specified by:
readVolumeData
in class VoxelReader
readVolumetricHeader
protected int readVolumetricHeader()
readTitleLines
protected void readTitleLines()
throws java.lang.Exception
- Throws:
java.lang.Exception
skipComments
protected int skipComments(boolean addToHeader)
throws java.lang.Exception
- Throws:
java.lang.Exception
readAtomCountAndOrigin
protected void readAtomCountAndOrigin()
throws java.lang.Exception
- Throws:
java.lang.Exception
readVoxelVector
protected void readVoxelVector(int voxelVectorIndex)
throws java.lang.Exception
- Throws:
java.lang.Exception
readExtraLine
protected int readExtraLine()
throws java.lang.Exception
- Throws:
java.lang.Exception
readVoxelData
protected void readVoxelData(boolean isMapData)
throws java.lang.Exception
- Specified by:
readVoxelData
in class VoxelReader
- Throws:
java.lang.Exception
skipVoxels
private void skipVoxels(int n)
throws java.lang.Exception
- Throws:
java.lang.Exception
getNextVoxelValue
protected float getNextVoxelValue(java.lang.StringBuffer sb)
throws java.lang.Exception
- Throws:
java.lang.Exception
nextVoxel
protected float nextVoxel()
throws java.lang.Exception
- Throws:
java.lang.Exception
gotoData
protected void gotoData(int n,
int nPoints)
throws java.lang.Exception
- Overrides:
gotoData
in class VoxelReader
- Throws:
java.lang.Exception
skipData
private void skipData(int nPoints)
throws java.lang.Exception
- Throws:
java.lang.Exception
countData
private int countData(java.lang.String str)
getTokens
java.lang.String[] getTokens()
parseFloat
float parseFloat()
parseFloat
float parseFloat(java.lang.String s)
parseFloatNext
float parseFloatNext(java.lang.String s)
parseInt
int parseInt()
parseInt
int parseInt(java.lang.String s)
parseIntNext
int parseIntNext(java.lang.String s)
parseInt
int parseInt(java.lang.String s,
int iStart)